UC San Diego Center for Computational Biology & Bioinformatics (@ucsd-ccbb)
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Top repositories

1

visJS2jupyter

visJS2jupyter is a tool to bring the interactivity of networks created with vis.js into jupyter notebook cells
Jupyter Notebook
78
star
2

VAPr

VAPr: A Python package for NoSQL variant data storage, annotation and prioritization
Python
34
star
3

NetColoc

development of network co-localization tool
Jupyter Notebook
13
star
4

C-VIEW

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
Python
9
star
5

cirrus-ngs

Python
8
star
6

gsia

Gene Set Information Analysis
R
6
star
7

jupyter-pathway

Canonical pathway visualization and analysis
Jupyter Notebook
5
star
8

mali-dual-crispr-pipeline

This repository contains code for the dual-CRISPR screen analysis pipeline developed to analyze results from the dual-CRISPR screening system set up by the labs of Dr. Prashant Mali and Dr. Trey Ideker. The software is developed by Amanda Birmingham and Roman Sasik of the Center for Computational Biology and Bioinformatics at the University of California, San Diego.
Python
4
star
9

qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
Python
3
star
10

ASD_combined_network_analysis

Notebooks from ASD-CHD combined network analysis paper
Jupyter Notebook
2
star
11

MPN_atlas_methods

Source code for methods for A Dynamic Pre-Leukemia Stem Cell Atlas of Myeloproliferative Neoplasm Evolution
Jupyter Notebook
2
star
12

network_bio_toolkit

toolbox of network biology methods
Jupyter Notebook
1
star
13

shinyGWAS

visualization for GWAS. Mostly based on outputs from FUMA
Jupyter Notebook
1
star